[Chimera-users] What do you do for comparative modeling if the pdb is so new it's not in UniProt?

[Elaine Meng]

Also, if you open a structure from the PDB in Chimera, then you can just use the Chimera menu: Favorites... Sequence to show the sequence of any/all of its biopolymer chains.

Elaine


> On Apr 30, 2021, at 9:27 AM, Marco Sette <sette at uniroma2.it> wrote:
> 
> If you search for the sequences the PDB Data Bank (RCSB) provides both the pdb file and the sequence in fasta format.
> 
> Best regards,
> 
> Marco
> 
> Il 30/04/2021 17:59, Ralph Loring ha scritto:
>> Hi,
>> I'm very new to Chimera and have been working through the tutorials, including the Comparative Modeling Tutorial.  However I'm stumped.  I'm interested in modeling chimeric proteins that involve the following pdbs: PDB 7KOO, 7KOX and 7KOQ and I can't get the sequence in my chimera to align with the template structure in the pdbs.  The problem is that the template pdbs only came out in April and are not yet included in UniProt.  They are deposited in RSCB and EMDB, but these don't appear to be alignment options in Chimera.  Do I need to appeal to UniProt, or is there an alternative way to make the association between the sequence and the structure?  Any additional tutorials on using MAV would be helpful as there seem to be a lot of editing features that are not explored in your tutorial.
>> Thanks for your help,
>> 
>> Ralph Loring
>> Associate Professor of Pharmacology
>> Department of Pharmaceutical Sciences
>> Northeastern University
>> 360 Huntington Avenue 
>> Boston, MA 02115 USA
>> 617-373-3216 office
>> 617-373-8886 fax
>> r.loring at northeastern.edu
>> 
>> 
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